Are you talking about your PHP code?If so,you will maybe need to change some path (if there are any in your code) since stuff like "C:\test.test" wont work in Linux.Other than that I think it should work.Never had any problems so far with my php code on Linux <=> Windows.

there is really only few differences that i know of
- on usage of the system functions system(), exec(), passthru() ...
- on usage of slashes. for winxx you sometimes even need double-backslashes on php (like in c) and sometimes you get them from functions (file upload eg.)
- on linux you have to deal with file and directory permissions now. this is not related to php directly, but is a UNIX thing. if you create / copy / move files in your scripts, they probably won´t work out-of-the-box.
- no COM support for linux (who needs this anyway?)

in general i think moving from windows to linux will make things work better. afaik php runs best and supports the most libraries on linux.